I think that ChribbaX's comparison of Dust BPOs to EVE T2 BPOs is a very good analogy--the problem mostly boils down to jealousy, and doesn't have much of an effect on the economy. Assuming manufacturing is even brought to Dust, having Dust BPOs function the same way as T2 BPOs in EVE pretty much solves everyone's problems (except the jellies). Also, I'm almost certainly not going to participate in manufacturing when/if it's available, and I'm sure the same is true for other mercs, so again, any feared, massive upset to the (as yet non-existent) economy seems a little premature.
Many people say that BPOs undermine the notion of "Risk vs. ISK". I do not think this is the case because, as other posters have mentioned, running BPOs is suboptimal for maintaining or improving one's KDR; since KDR (and WP, and possibly other numbers
if CCP ever introduces more robust statistics) is also quite important to numerous players, they are inclined to run higher-tiered gear as running BPOs (ie, militia and standard level gear) definitely increases the
risk of marring one's stats. It think most folks here will agree that, for the most part, the better gear a merc fits, the better the merc typically performs.
It's also worth noting that until at least the middle or end of January, the 'Exile' Assault Rifle BPO was available on the marketplace, via whatever AUR pack it came in. So, at least one BPO was available well after CCP started changing their stance on them and people started to get their feathers ruffled.
Since it does mostly seem to be an issue of jealousy, I'd say there's a few reasonable solutions. 1) What ChribbaX suggested; 2) make BPOs non-tradeable and have future events/marketplace packs where newer players can procure them (this mitigates jealousy, and since a 'Dren' AR = 'Exile' AR = 'Toxic' AR with different skins, who really cares?); 3) reinstate BPOs as normal, AUR-purchasable items, making them unusable for manufacturing or trading (this way, any Dust-side Ash Ketchums can collect 'em all and everyone feels warm fuzzies for being treated the same, regardless of when they started playing).
Or, here's an even more daring thought (but it requires CCP to provide a complete set of racial heavy weapons): since starter fits suck bwawls anyway, why not grant each merc a set of racial basic/standard level BPOs for building out whatever suits they dern well please? This would make selecting a race somewhat more significant (it determines what your free, "starter" BPOs will be), would remove the worthless starter fits from the game, and would make basic gear more relevant. If every new merc started the game with a set of racial BPOs (say, a basic suit in each size with a basic 'nade, racial light, heavy, and sidearm weapons; race-aligned tanking mods, etc.) they could mix and match, and it would make the new player experience much better, since trying to put together a fit with the starter suits is next to impossible without decent skills. Of course, all these BPOs would be available on the market, so interested parties could acquire each race's BPOs.